Contacts of the strand formed by residues 285 - 292 (chain D) in PDB entry 1UHG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241D MET* 5.7 3.1 - - - +
282D LEU* 5.0 4.9 - - - -
283D PRO* 3.4 26.5 - - + +
284D ARG* 1.3 75.8 - - - +
286D LYS* 1.3 64.5 + - - +
287D MET* 4.0 14.1 - - + -
332D ALA 4.7 0.2 - - - -
333D GLU* 3.4 6.6 - - - +
334D ILE* 2.7 58.6 + - + +
364D PHE* 3.9 18.4 - - + -
366D PHE* 3.6 41.1 - - + -
382D CYS* 3.9 18.4 - - + -
385D PRO* 3.8 13.9 - - + +
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Residues in contact with LYS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASN* 5.8 1.2 + - - -
284D ARG* 4.3 6.7 - - + +
285D MET* 1.3 78.7 - - - +
287D MET* 1.3 64.6 + - - +
288D GLU 4.1 0.7 + - - -
331D HIS* 5.6 11.0 - - + -
332D ALA 3.8 4.5 - - - -
333D GLU* 3.5 30.7 - - + +
384D SER 5.6 0.2 - - - +
385D PRO* 3.6 14.2 + - - +
3402D SO4 2.9 42.2 + - - -
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Residues in contact with MET 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASN* 3.9 22.9 - - + -
27D ILE 3.7 23.3 - - - +
28D PHE* 3.8 23.1 - - + -
285D MET* 4.0 29.6 - - + -
286D LYS* 1.3 77.5 - - - +
288D GLU* 1.3 63.6 + - - +
289D GLU* 5.5 0.9 - - - +
331D HIS* 3.1 7.9 + - - -
332D ALA* 2.8 44.7 + - + +
334D ILE* 5.8 2.5 - - + -
366D PHE* 3.7 27.8 - - + -
381D ARG 3.7 13.5 - - - +
382D CYS* 4.6 7.6 - - - -
384D SER 5.1 2.2 - - - +
385D PRO* 5.3 0.7 - - - +
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Residues in contact with GLU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE* 4.8 0.2 - - - -
156D ILE* 3.8 20.1 - - - +
157D ILE* 4.7 11.8 - - + +
158D ARG* 5.3 1.6 + - - -
286D LYS 4.1 1.0 + - - -
287D MET* 1.3 76.2 - - - +
289D GLU* 1.3 86.6 + - - +
329D ALA* 6.0 2.2 - - + -
330D ALA 3.1 14.6 - - - +
331D HIS* 2.6 36.8 + - + +
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Residues in contact with GLU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D HIS* 5.9 0.9 + - - -
25D GLU* 5.2 5.1 - - - +
26D ASN* 3.5 38.3 + - + +
27D ILE 4.2 1.1 - - - -
28D PHE* 3.6 29.8 + - + +
287D MET* 5.6 0.2 - - + -
288D GLU* 1.3 93.4 + - - +
290D LYS* 1.3 61.7 + - - +
291D TYR* 3.3 31.8 + - + +
328D HIS 4.0 0.7 - - - +
329D ALA* 3.4 2.5 - - - +
330D ALA* 3.0 30.0 + - - -
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Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D HIS* 5.3 2.3 - - - -
157D ILE* 6.0 0.9 - - + -
158D ARG 4.8 2.4 + - - +
159D ASN* 3.0 26.9 + - - +
160D VAL* 3.5 28.5 + - + +
162D GLN* 3.8 22.8 + - - +
289D GLU* 1.3 75.8 + - - +
291D TYR* 1.3 75.8 + - - +
327D VAL* 3.5 21.8 - - + -
328D HIS 3.2 5.6 - - - +
329D ALA* 4.1 7.4 - - + +
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Residues in contact with TYR 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.9 27.1 - - + -
22D HIS* 3.7 37.2 - + - -
26D ASN 4.1 2.1 + - - -
27D ILE* 3.3 13.0 - - + +
28D PHE 3.1 45.1 + - - -
29D TYR* 4.1 14.6 - - + -
289D GLU* 3.3 23.4 - - + +
290D LYS* 1.3 81.6 - - - +
292D ASN* 1.3 61.7 + - - +
293D LEU* 3.1 8.0 + - + +
296D VAL* 4.7 10.3 - - + -
327D VAL* 3.5 7.5 - - - +
328D HIS* 2.7 50.3 + + + +
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Residues in contact with ASN 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D TYR* 1.3 70.1 - - - +
293D LEU* 1.3 59.3 + - - +
294D THR* 3.1 17.5 + - - -
295D SER* 2.9 26.0 + - - +
296D VAL* 3.3 10.8 + - - +
325D GLN* 5.1 0.9 - - - +
326D ALA 3.8 6.1 - - - +
327D VAL* 4.9 2.0 - - - +
386D NAG 1.4 64.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il